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Idea #13192
closed
Update SGLF sanity checking CWL and parallelize
Start date:
03/14/2018
Due date:
Story points:
-
Description
There is a new sglf-check program to do some sanity checks on an SGLF file. Incorporate this program into the CWL sglf-sanity-check pipeline.
Also, the CWL sglf-sanity-check pipeline is serial. Parallelize this workflow to reduce clock time of the check.
I think the best method is to split in groups of tilepaths, so process N tilepaths per node allocated.
Updated by Abram Connelly about 6 years ago
- Status changed from New to In Progress
Updated by Sarah Zaranek about 6 years ago
SWZ reviewed repo:
Need to remove test directory:
++ b/cwl-version/l7g-tile-lib/sglf-sanity-check/src/.tmp/test.list
/data-sdd/data/sglf/0000.sglf.gz...
And this directory:
+++ b/tools/tile-lib/tests/data/035e-bad-tileid-0.sglf
Updated by Abram Connelly about 6 years ago
The .tmp directory has been removed.
The 035e-bad-tileid-0.sglf has been kept as that's a working test file. See the sglf-check-tests.sh file.
Updated by Abram Connelly about 6 years ago
- Status changed from In Progress to Resolved
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